NGS Meeting on 18-12-2009

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Discussions and updates

  • Please follow links in the Agenda section to obtain the slides.
  • A local Galaxy instance is running at Morris' group in UMCG.
  • Bowtie supports color space reads now
  • Frans reported Maq and Bowtie as good alignment tools. Maq is already supported by the NBIC Life Science Grid Portal.
  • Matt wrapped GAPSS as a Galaxy toolbox.

We reached the following agreements:

  • Galaxy is agreed by the team as the common platform to share and integrate home-made tools and workflows. At the moment, NBIC research team is investigating into the possibilities and requirements to have a local instance of Galaxy. We will present some status update on the next NGS meeting.
  • We will improve the Bio-Assist wiki page about NGS tools evaluation. We will also look into the possibilities to reach a broader audience, e.g. in WikiPedia and SEQanswers.
    1. Jan and Leon will work on the section about assembly.
    2. Frans and Leon will work on the section about alignment and SNP detection. Contributions from others are highly encouraged.
  • A next meeting will be on 15-1-2010 before the regular Bio-Assist meeting. In that meeting, we will set up a further meeting/collaboration plan. A possibility is to rotate the meeting location among the participating groups.


The goal of this meeting is the following:

  • introduce the opportunities in the NBIC NGS platform
  • exchange information about (home made) software/methods
  • seek for a common platform to share the workflows
  • set up a further collaboration plan

Each responsible person will lead the discussion on one subject. Preparing slides are not mandatory but nice to have.

Time slot Responsible Subject
9:00-9:10 Leon Mei Introduction to the NBIC NGS Platform plan
9:10-9:30 Jan van Haarst De novo assembly software
9:30-9:50 Frans Paul Ruzius Benchmarking and comparison of mapping assembly software ( Report)
9:50-10:10 Matt Hestand Generic pipelines and possibility on using one platform (e.g., Galaxy, Taverna) to share work flows/pipelines
10:10-10:15 Leon Mei Closing


Surf meeting room

Hojel City Center, gebouw D (5th floor)

Graadt van Roggenweg 340

3531 AH Utrecht


9:00-10:15, 18 December 2009 (before the main BioAssist programmer meeting)


  • Jan van Haarst (Plant Research International, Wageningen)
  • Matt Hestand (LUMC, Leiden)
  • Victor de Jager (NBIC, Nijmegen)
  • Leon Mei (NBIC, Rotterdam)
  • Barbera van Schaik (AMC, Amsterdam)
  • Marcel Willemsen (AMC, Amsterdam)
  • Joris Lops (UMCG, Groningen)
  • Morris Swertz (UMCG, Groningen)
  • Frans Paul Ruzius (Hubrecht Institute, Utrecht)
  • Wilfred van IJcken (EMC, Rotterdam)
  • Stephan Nouwens (EMC, Rotterdam)
  • Jurgen Piet (AMC, Amsterdam)
  • Marc van Driel (NBIC)
  • Rob Hooft (NBIC)
  • Marco Roos (LUMC, Leiden)
  • Machiel Jansen (SARA, Amsterdam)